Since they regrow now, I trample them carelessly all the time - the ones that line my paths anyway. But I still can't break the habit of never running on grass.
Since I've been traumatized by New Leaf where if you run over a flower it dies all together, I try my best not to trample them. I only trampled a few thankfully.
I've trampled a couple because I forget I have a patch of flowers somewhere until it's too late. New Leaf has trained me pretty well though since I usually walk everywhere.
Three sections of my beach are entirely filled with flowers, and I really need to do something about that. I've trampled way too many when looking for the two daily DIY bottles. And since they don't regrow on sand, there's just a bunch of buds everywhere. It makes it a little bit harder when I'm looking for specific flowers.
It has happened a few times since launch, but I haven't really kept track of how many times. It happens more often when a friend visits, since I don't really run in flowered areas, but since the flowers aren't fully destroyed like they were in past games, it doesn't bother me much at all. At the same time, contradictory as it is to what I just said, I wish we actually could still destroy the flowers entirely by trampling. It's a pain to have to dig them up and sell them or throw them away when it was so simple to destroy them in the older games.